Merge pull request #241 from phac-nml/fix/ci

Fix GitHub CI Tests
phac-nml · Sep 14, 2023 · 1a2d7c4 · 1a2d7c4
2 parents e752f6e + 73e8d93
commit 1a2d7c4
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diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -1,13 +1,24 @@
-name: Galaxy Tool Linting and Tests for Push and PR
+name: Galaxy Tool Linting and Tests for push and PR
 on:
- pull_request: # Run on all PRs
+ pull_request:
+ paths-ignore:
+ - '.github/**'
+ - 'deprecated/**'
+ - 'docs/**'
+ - '*'
  push:
- branches: # Run on any push to development or master
+ branches:
  - development
+ - main
  - master
+ paths-ignore:
+ - '.github/**'
+ - 'deprecated/**'
+ - 'docs/**'
+ - '*'
 env:
  GALAXY_FORK: galaxyproject
- GALAXY_BRANCH: release_22.05
+ GALAXY_BRANCH: release_23.1
  MAX_CHUNKS: 4
  MAX_FILE_SIZE: 1M
 concurrency:
@@ -49,17 +60,17 @@ jobs:
  - name: Determine latest commit in the Galaxy repo
  id: get-galaxy-sha
  run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Cache .cache/pip
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-pip
  with:
  path: ~/.cache/pip
  key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
  - name: Cache .planemo
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-planemo
  with:
  path: ~/.planemo
@@ -70,7 +81,7 @@ jobs:
  run: pip install wheel
  - name: Install flake8
  run: pip install flake8 flake8-import-order
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 0
  - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -103,26 +114,36 @@ jobs:
  matrix:
  python-version: ['3.7']
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 1
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Cache .cache/pip
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-pip
  with:
  path: ~/.cache/pip
  key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+
+ - name: Set fail level for pull request
+ if: ${{ github.event_name == 'pull_request' }}
+ run:
+ echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
+ - name: Set fail level for merge
+ if: ${{ github.event_name != 'pull_request' }}
+ run:
+ echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
  - name: Planemo lint
  uses: galaxyproject/planemo-ci-action@v1
  id: lint
  with:
  mode: lint
+ fail-level: ${{ env.FAIL_LEVEL }}
  repository-list: ${{ needs.setup.outputs.repository-list }}
  tool-list: ${{ needs.setup.outputs.tool-list }}
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
  if: ${{ failure() }}
  with:
  name: 'Tool linting output'
@@ -132,21 +153,21 @@ jobs:
  flake8:
  name: Lint Python scripts
  needs: setup
- if: ${{ needs.setup.outputs.repository-list != '' }}
+ if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
  runs-on: ubuntu-latest
  strategy:
  fail-fast: false
  matrix:
  python-version: ['3.7']
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 1
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Cache .cache/pip
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-pip
  with:
  path: ~/.cache/pip
@@ -155,7 +176,7 @@ jobs:
  run: pip install flake8 flake8-import-order
  - name: Flake8
  run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
  if: ${{ failure() }}
  with:
  name: 'Python linting output'
@@ -164,21 +185,21 @@ jobs:
  lintr:
  name: Lint R scripts
  needs: setup
- if: ${{ needs.setup.outputs.repository-list != '' }}
+ if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
  os: [ubuntu-20.04]
  r-version: ['release']
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 1
  - uses: r-lib/actions/setup-r@v2
  with:
  r-version: ${{ matrix.r-version }}
  - name: Cache R packages
- uses: actions/cache@v2
+ uses: actions/cache@v3
  with:
  path: ${{ env.R_LIBS_USER }}
  key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
@@ -194,7 +215,7 @@ jobs:
  - name: lintr
  run: |
  library(lintr)
- linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
+ linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
  con <- file("repository_list.txt", "r")
  status <- 0
  while (TRUE) {
@@ -214,7 +235,7 @@ jobs:
  }
  quit(status = status)
  shell: Rscript {0}
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
  if: ${{ failure() }}
  with:
  name: 'R linting output'
@@ -226,7 +247,7 @@ jobs:
  if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 0
  - name: Check file sizes
@@ -241,7 +262,7 @@ jobs:
  cat file_size_report.txt
  exit 1
  fi
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
  if: ${{ failure() }}
  with:
  name: 'File size report'
@@ -269,27 +290,29 @@ jobs:
  ports:
  - 5432:5432
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 1
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Cache .cache/pip
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-pip
  with:
  path: ~/.cache/pip
  key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
  - name: Cache .planemo
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-planemo
  with:
  path: ~/.planemo
  key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
  - name: Get number of CPU cores
  uses: SimenB/github-actions-cpu-cores@v1
  id: cpu-cores
+ - name: Clean dotnet folder for space
+ run: rm -Rf /usr/share/dotnet
  - name: Planemo test
  uses: galaxyproject/planemo-ci-action@v1
  id: test
@@ -302,8 +325,8 @@ jobs:
  chunk-count: ${{ needs.setup.outputs.chunk-count }}
  galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
  # Limit each test to 15 minutes
- test_timeout: 900
- - uses: actions/upload-artifact@v2
+ test_timeout: 1800
+ - uses: actions/upload-artifact@v3
  with:
  name: 'Tool test output ${{ matrix.chunk }}'
  path: upload
@@ -316,20 +339,20 @@ jobs:
  combine_outputs:
  name: Combine chunked test results
  needs: [setup, test]
- if: ${{ needs.setup.outputs.repository-list != '' }}
+ if: ${{ always() && needs.setup.outputs.repository-list != '' }}
  runs-on: ubuntu-latest
  strategy:
  matrix:
  python-version: ['3.7']
  steps:
- - uses: actions/download-artifact@v2
+ - uses: actions/download-artifact@v3
  with:
  path: artifacts
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Cache .cache/pip
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-pip
  with:
  path: ~/.cache/pip
@@ -340,7 +363,7 @@ jobs:
  with:
  mode: combine
  html-report: true
- - uses: actions/upload-artifact@v2
+ - uses: actions/upload-artifact@v3
  with:
  name: 'All tool test results'
  path: upload
@@ -349,25 +372,31 @@ jobs:
  id: check
  with:
  mode: check
+ - name: Check if all test chunks succeeded
+ run: |
+ NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+ if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
+ exit 1
+ fi
 
  # deploy the tools to the toolsheds (first TTS for testing)
  deploy:
  name: Deploy
- needs: [setup, lint, flake8, lintr, combine_outputs]
+ needs: [setup, lint, combine_outputs]
  if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'phac-nml' }}
  runs-on: ubuntu-latest
  strategy:
  matrix:
  python-version: ['3.7']
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  with:
  fetch-depth: 1
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Cache .cache/pip
- uses: actions/cache@v2
+ uses: actions/cache@v3
  id: cache-pip
  with:
  path: ~/.cache/pip
@@ -388,6 +417,28 @@ jobs:
  shed-target: toolshed
  shed-key: ${{ secrets.TS_API_KEY }}
 
+ deploy-report:
+ name: Report deploy status
+ needs: [deploy]
+ if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'phac-nml' }}
+ runs-on: ubuntu-latest
+ steps:
+ # report to the PR if deployment failed
+ - name: Get PR object
+ uses: 8BitJonny/[email protected]
+ id: getpr
+ with:
+ sha: ${{ github.event.after }}
+ - name: Create comment
+ uses: peter-evans/create-or-update-comment@v2
+ with:
+ token: ${{ secrets.PAT }}
+ issue-number: ${{ steps.getpr.outputs.number }}
+ body: |
+ Attention: deployment ${{ needs.deploy.result }}!
+
+ https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
  determine-success:
  name: Check workflow success
  needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
@@ -409,4 +460,3 @@ jobs:
  - name: Check tool test status
  if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
  run: exit 1
-